[gmx-users] nitrogen itp file with virtual site

[Ali Ahmed]

Dear Justin
I have tried same what you have said. I followed the tutorial for CO2 but
didn't work, gave an error during the energy minimization . I'm not sure
what was the wrong, I noticed the N atoms (in the box) were separated from
the virtual site after the error.


On Mon, Jul 17, 2017 at 10:41 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/17/17 11:38 AM, Ali Ahmed wrote:
>
>> Dear Justin
>> Thank you very much. As I saw in some literature (as in the link below)
>> that N atom has a negative charge and needs a massless positive charge. I
>> tried with most of the FFs but could not produce nitrogen density above
>> critical point. I don'n know which FF is the best one and I'm new to MD
>> simulations and new GROMACS user.
>> Could you please tell me which FF should I use?
>>
>
> What you're citing is a custom model.  You can write the force field files
> very easily.  I see what you're trying to do now, but you should be clear
> that N2 is not a negatively charged molecule simply because the N atoms (in
> this representation) have partial negative charges.  The virtual site
> balances it out so that electrostatic properties are better represented.
>
> The virtual site you need to create is a simple one, placed at the center
> of the N-N bond, so this is virtual_sites2 with an "a" value of 0.5.
>
> -Justin
>
>
> Thank you very much I appreciate your support.
>>
>> http://iopscience.iop.org/article/10.1088/0965-0393/24/4/045002/meta
>>
>> On Mon, Jul 17, 2017 at 8:40 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 7/16/17 9:20 PM, Ali Ahmed wrote:
>>>
>>> Hello GROMACS users,
>>>> This is Ali, I'm new to Gromacs and doing MD simulation of nitrogen at
>>>> super critical point.The structure I use is different from regular
>>>> nitrogen
>>>> (N-N). As you know N atom has a negative charge which means the nitrogen
>>>> molecule will be negatively charged, therefore I need to use massless
>>>> and
>>>>
>>>>
>>> This is incorrect - N2 carries no formal charge.
>>>
>>> charged virtual site to equilibrate the molecule. I have looked on the
>>>
>>>> tutorial about CO2 to produce the XXX.itp but didnot work with me. Could
>>>> anyone have done it before tell me how to do it ?
>>>>
>>>>
>>>> You don't need virtual sites for a diatomic molecule.
>>>
>>> -Justin
>>>
>>> Here are the parameters:
>>>
>>>> N :mass =14.0067, epsilon =(0.3026 KJ/mol), sigma =(0.332 nm), Charge
>>>> =(-0.482 e).
>>>>
>>>> XX (massless, charged particle ):mass =0, epsilon=0, sigma=0 Charge=
>>>> 0.964
>>>> e.
>>>>
>>>> Thank you very much.
>>>>
>>>>
>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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